To address the challenges posed by the unique characteristics of ship-specific loads, such as propulsion and pulsed loads, the configuration of a hybrid energy storage system (HESS) has become an effective approach to enhance the performance of ship power systems. However, existing hybrid energy storage power management strategies (PMS) rely on fixed thresholds or cutoff frequencies to separate high- and low-frequency power components, making them difficult to adapt to dynamic ship load variations. This often leads to improper power sharing between energy-type and power-type storage units, accelerating system degradation and ultimately limiting the durability and economic performance of ship power systems. Therefore, this paper proposes a multi-time scale power management strategy for ship power systems considering durability and reliability. First, a multi-objective optimization model based on the endurance of generators and the HESS is constructed on a long-time scale, and the non-dominated sorting algorithm is employed to solve the proposed model, which improves the durability of ship power systems. To overcome the limitations of traditional boundary line-based PMS, an adaptive boundary domain PMS based on variational mode decomposition is proposed at the short-time scale. This strategy decomposes the HESS power into high-, medium-, and low-frequency components. The high-frequency component is allocated to the supercapacitor, the low-frequency component to the battery, and the medium-frequency component is shared by both, enhancing the rationality of power distribution and extending the service life of the energy storage units. Finally, simulation results verify the effectiveness of the proposed strategy in improving the operational durability, reliability, and economy of the ship power systems.